Jules Muis, a former Ernst & Young partner, who was responsible for revamping the audit and financial control system at the World Bank, announced his resignation in a letter to administrative reform commissioner Neil Kinnock earlier this month.

Muis has been with the commission for two and a half years and said he would stand down next April.

Responding to the announcement, shadow chancellor Michael Howard said: ‘The fact that the EU’s chief auditor resigned as he was being prevented from mounting a thorough inquiry onto fraud shows quite how bad the problems are at the European Commission.

‘What is Gordon Brown doing to put a stop to this EC fraud for which the British taxpayer is paying?’